Jean — Molecular Biology & Genomics

call_mixed_bases_from_trace

Read-only

Call the bases of a Sanger trace AND ask at every position whether a second allele is present, writing a two-base IUB code (R, Y, S, W, K, M) where it is.

Input Schema

Name	Required	Description	Default
`mode`	No	het = the two alleles are assumed present 1:1 (a diploid heterozygote); mix = no assumption is made about their ratio.	het
`table`	No	the instrument/polymer calibration table to score against. The same signal scores differently under each, so a quality value is only interpretable with the table named. Defaults to ABI 3730 POP-7.	3730pop7
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
`document`	No	which trace to run on: a file name (`read_F.ab1`) or its project file id. Leave unset to use the trace tab on screen. A file id is project-specific, so a template ships this unset.
`min_ratio`	No	how tall a second peak must be, as a fraction of the called peak, before the search will consider it as a second allele. Lowering it widens what is considered, which is not the same as calling more mixed bases.

Output Schema

Name	Required	Description
`bases`	Yes	how many bases the reading called
`mixedBases`	Yes	how many positions were called as carrying two alleles. Reported as 0 rather than omitted when none were, because a missing field is not an answer
`meanQuality`	Yes	the mean Phred of the reading, on the calibration table it names
`instrumentBases`	Yes	how many the FILE carries, so a gate can see a de-novo reading change the read's length

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.5/5.0

Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare this a safe read-only, non-destructive, non-open-world operation, so the description need not restate safety. It adds real behavior beyond them by naming the output convention (R, Y, S, W, K, M written only where a second allele is present), but says nothing about thresholds, failure modes, or how results are reported beyond the output schema.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single front-loaded sentence with no filler, and the key concept (two-base IUB output) arrives early. The capitalized 'AND' is a slightly awkward emphasis device, but it does signal that this tool does more than plain base calling.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema present and annotations covering safety, the description only needs to convey what the tool produces and how it differs from plain calling, which it largely does via the IUB code explanation. The remaining gap is the unstated relationship to call_bases_from_trace and no hint that a trace must be selected via document or the on-screen trace tab.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100% — mode, table, document, and min_ratio all carry their own explanatory text, including the important caveat that lowering min_ratio widens the search rather than calling more mixed bases. The description adds no parameter-level meaning over the schema, so the baseline of 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource (base-calling a Sanger trace) plus the distinguishing behavior: it also interrogates every position for a second allele and emits IUB ambiguity codes. That makes it separable from call_bases_from_trace without opening either schema, though the sibling is never named explicitly.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Usage is only implied: the tool is for detecting mixed/heterozygous positions in a trace, so an agent can infer it is the option to pick when ambiguity matters. There is no explicit when-to-use, when-not-to-use, or pointer to call_bases_from_trace as the plain-calling alternative.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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